Neck Shaping Done

I have got the neck shaped and finished now ready to fit the saddle,nut etc.

I have enrolled in a French Polishing course.The teacher actually build guitars so this should be pretty good.

I bolted the neck on tonight and I have a small problem.The neck/ fretboard was sitting up about 1.5mm off the top.

My first thought is to file the holes out a bit so it will sit down.I have asked the guys on .Guitar Kit Forum for their opinion